Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions

2009 ◽  
Vol 113 (10) ◽  
pp. 3112-3128 ◽  
Author(s):  
Maria M. Reif ◽  
Vincent Kräutler ◽  
Mika A. Kastenholz ◽  
Xavier Daura ◽  
Philippe H. Hünenberger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Dynamics Simulations

scholarly journals SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure

2019 ◽  
Vol 24 (9) ◽  
pp. 928-938 ◽  
Author(s):  
Luca Palazzolo ◽  
Chiara Paravicini ◽  
Tommaso Laurenzi ◽  
Sara Adobati ◽  
Simona Saporiti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Amino Acid ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Amino Acid Residues ◽  
Dibasic Amino Acid ◽  
Novel Target ◽  
Function Relationship ◽  
Dynamics Simulations

SLC6A14 (ATB0,+) is a sodium- and chloride-dependent neutral and dibasic amino acid transporter that regulates the distribution of amino acids across cell membranes. The transporter is overexpressed in many human cancers characterized by an increased demand for amino acids; as such, it was recently acknowledged as a novel target for cancer therapy. The knowledge on the molecular mechanism of SLC6A14 transport is still limited, but some elegant studies on related transporters report the involvement of the 12 transmembrane α-helices in the transport mechanism, and describe structural rearrangements mediated by electrostatic interactions with some pivotal gating residues. In the present work, we constructed a SLC6A14 model in outward-facing conformation via homology modeling and used molecular dynamics simulations to predict amino acid residues critical for substrate recognition and translocation. We docked the proteinogenic amino acids and other known substrates in the SLC6A14 binding site to study both gating regions and the exposed residues involved in transport. Interestingly, some of these residues correspond to those previously identified in other LeuT-fold transporters; however, we could also identify a novel relevant residue with such function. For the first time, by combined approaches of molecular docking and molecular dynamics simulations, we highlight the potential role of these residues in neutral amino acid transport. This novel information unravels new aspects of the human SLC6A14 structure–function relationship and may have important outcomes for cancer treatment through the design of novel inhibitors of SLC6A14-mediated transport.

Local order and long range correlations in imidazolium halide ionic liquids: a combined molecular dynamics and XAS study

2015 ◽  
Vol 17 (25) ◽  
pp. 16443-16453 ◽  
Author(s):  
Valentina Migliorati ◽  
Alessandra Serva ◽  
Giuliana Aquilanti ◽  
Sakura Pascarelli ◽  
Paola D'Angelo
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Long Range ◽  
Exafs Spectroscopy ◽  
Local Order ◽  
Long Range Correlations ◽  
Long Range Interactions ◽  
Dynamics Simulations

EXAFS spectroscopy and molecular dynamics simulations have been combined to unveil the effect of the cation and anion nature on the local order and long range interactions of imidazolium halide ionic liquids.

Atomic Migration in Bulk and Thin Film L10 Alloys: Experiments and Molecular Dynamics Simulations

2007 ◽  
Vol 263 ◽  
pp. 41-50 ◽  
Author(s):  
Veronique Pierron-Bohnes ◽  
R.V.P. Montsouka ◽  
Christine Goyhenex ◽  
T. Mehaddene ◽  
Leila Messad ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Long Range ◽  
Range Order ◽  
Magnetic Storage ◽  
Thermodynamic Quantities ◽  
Long Range Order ◽  
Tight Binding Approximation ◽  
Densities Of States ◽  
Dynamics Simulations

Ferromagnetic L10 ordered alloys are extensively studied nowadays as good candidates for high density magnetic storage media due to their high magnetic anisotropy, related to their chemical order anisotropy. Epitaxial thin bilayers NiPt/FePt/MgO(001) have been grown at 700 K and annealed at 800 K and 900 K. At 800 K, the L10 long-range order increases without measurable interdiffusion. At 900 K, the interdiffusion takes place without destroying the L10 long-range order. This surprising observation can be explained by different diffusion mechanisms that are energetically compared using molecular dynamics simulations in CoPt in the second moment tight binding approximation. In addition, the frequencies of the normal modes of vibration have been measured in FePd, CoPt and FePt single crystals using inelastic neutron scattering. The measurements were performed in the L10 ordered structure at 300 K. From a Born-von Karman fit, we have calculated the phonon densities of states. The migration energies in the 3 systems have been estimated using the model developed by Schober et al. (1981). The phonon densities of states have also been used to calculate several thermodynamic quantities as the vibration entropy and the Debye temperature.

Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations

2005 ◽  
Vol 127 (2) ◽  
pp. 476-477 ◽  
Author(s):  
Matthew M. Dedmon ◽  
Kresten Lindorff-Larsen ◽  
John Christodoulou ◽  
Michele Vendruscolo ◽  
Christopher M. Dobson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Long Range ◽  
Spin Label ◽  
Long Range Interactions ◽  
Dynamics Simulations
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